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Crystal structure of human CRFR2 alpha extracellular domain in complex with urocortin 1
Analyse Crystal structure of human CRFR2 alpha extracellular domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N96
- Type
- protein
- Length
- 1,935 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose binding protein-CRFR2 alpha; Urocortin
- UniProt
- P55089
- Ligands
- GLC, NH2
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose binding protein-CRFR2 alpha | protein | 473 | 40% helix, 22% strand | — |
| B | Maltose binding protein-CRFR2 alpha | protein | 471 | 40% helix, 22% strand | — |
| C | Maltose binding protein-CRFR2 alpha | protein | 467 | 41% helix, 22% strand | — |
| D | Maltose binding protein-CRFR2 alpha | protein | 468 | 42% helix, 22% strand | — |
| E, F | Urocortin | protein | 16 | 88% helix, 0% strand | P55089 |
| G | Urocortin | protein | 14 | 71% helix, 0% strand | P55089 |
| H | Urocortin | protein | 10 | 70% helix, 0% strand | P55089 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- NH2 · Amino group · ion · 4 copies · chains C, E, D, F, A, G, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.81 | 0.82 | 101 | GLC |
| 2 | 589 | 0.81 | 0.86 | 66 | GLC |
| 3 | 683 | 0.79 | 0.84 | 79 | empty |
| 4 | 769 | 0.72 | 0.78 | 49 | empty |
| 5 | 292 | 0.71 | 0.85 | 32 | GLC |
Interfaces
8 interfaces between chains.
- B–C · 1604 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1602 Ų buried · 12 hydrogen bonds · protein-protein
- A–G · 871 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 830 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 818 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3N96 · Crystal structure of human CRFR2 alpha extracellular domain in complex with Urocortin 1 · the same entry in another collection · chain H against H, TM-score 1.00
- P55089 · AlphaFold monomer V2.0 prediction for urocortin (P55089) · a predicted model of the same protein · chain H against A, TM-score 0.76
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P55089
- Elsewhere: RCSB PDB 3N96 · PDBe 3N96 · UniProt P55089
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